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Real-time $R_t$ of COVID-19 pandemic in Texas (Until Sep 27)

This report estimates the county level real-time effective production number ($R_t$) of the COVID-19 pandemic in Texas, based on data from the Texas Health and Human Services. This report is updated daily with the most recent version available at the ICTR website.

This report is created and maintained by data scientists from the Institute for Clinical & Translational Research, Baylor College of Medicine, with an algorithm that is based on Kevin Systrom's work for the US data. Please refer to the original report for details.

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-13-d7398d2bbf00> in <module>
      1 # Note that this takes a while to execute - it's not the most efficient algorithm
----> 2 hdis = highest_density_interval(posteriors, p=.9)
      3 
      4 most_likely = posteriors.idxmax().rename('ML')
      5 

<ipython-input-8-3ebab98da991> in highest_density_interval(pmf, p, debug)
      2     # If we pass a DataFrame, just call this recursively on the columns
      3     if(isinstance(pmf, pd.DataFrame)):
----> 4         return pd.DataFrame([highest_density_interval(pmf[col], p=p) for col in pmf],
      5                             index=pmf.columns)
      6 

<ipython-input-8-3ebab98da991> in <listcomp>(.0)
      2     # If we pass a DataFrame, just call this recursively on the columns
      3     if(isinstance(pmf, pd.DataFrame)):
----> 4         return pd.DataFrame([highest_density_interval(pmf[col], p=p) for col in pmf],
      5                             index=pmf.columns)
      6 

<ipython-input-8-3ebab98da991> in highest_density_interval(pmf, p, debug)
     14 
     15     # Find the smallest range (highest density)
---> 16     best = (highs - lows).argmin()
     17 
     18     low = pmf.index[lows[best]]

ValueError: attempt to get argmin of an empty sequence

Daily new cases and real time $R_t$ for Texas Medical Center

Here are estimated $R_t$ in the past 15 days:

ML Low_90 High_90
Collected Date
2020-09-10 0.92 0.53 1.25
2020-09-11 0.92 0.54 1.26
2020-09-12 0.90 0.52 1.24
2020-09-13 0.89 0.52 1.24
2020-09-14 0.89 0.49 1.22
2020-09-15 0.90 0.51 1.24
2020-09-16 0.90 0.51 1.24
2020-09-17 0.89 0.50 1.23
2020-09-18 0.86 0.45 1.19
2020-09-19 0.82 0.43 1.17
2020-09-20 0.78 0.37 1.12
2020-09-21 0.74 0.32 1.08
2020-09-22 0.68 0.27 1.04
2020-09-23 0.63 0.21 0.99
2020-09-24 0.56 0.13 0.92

Daily new cases and real time $R_t$ for Harris County

NOTE: New cases reported on September 16 (2768) includes cases in the past month that were not reported in time. The estimated real-time $R_t$ for September 16 is therefore inaccurate.

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-30-8b70bf670119> in <module>
      1 county_name = 'Harris'
      2 harris_result = [result for name, result in final_results.groupby('county')
----> 3     if name == county_name][0]
      4 
      5 fig, axes = plt.subplots(nrows=1, ncols=2, figsize=(15, 5))

IndexError: list index out of range

Here are estimated $R_t$ in the past 15 days:

Execution using papermill encountered an exception here and stopped:

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-31-ae5eb0a1d9c3> in <module>
----> 1 harris_result.tail(15)

NameError: name 'harris_result' is not defined

Daily new cases and real time $R_t$ for all Texas counties

Most recent $R_t$ by county